Proteopedia

Ribosome

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The Ribosome
The protein synthesis machine of cells
shown with the 3 transfer RNAs and messenger RNA bound.





IntroductionIntroduction

 
Drag the structure with the mouse to rotate
The Ribosome (1jgo and 1giy), resolution 5.5Å ().

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The ribosome is a complex composed of RNA and protein that adds up to several million daltons in size and plays a critical role in the process of decoding the genetic information stored in the genome into protein as outlined in what is now known as the Central Dogma of Molecular Biology. Specifically, the ribosome carries out the process of translation, decoding the genetic information encoded in messenger RNA, one amino acid at a time, into newly synthesized polypeptide chains.

Nobel Prize Winners and Other ContributorsNobel Prize Winners and Other Contributors

Venkatraman Ramakrishnan of the M.R.C. Laboratory of Molecular Biology in Cambridge, England; Thomas A. Steitz of Yale University; and Ada E. Yonath of the Weizmann Institute of Science in Rehovot, Israel have been awarded the the 2009 Nobel Prize in Chemistry[1] for their landmark work revealing the atomic details of the molecular machine that make proteins in all cells, the ribosome. Their findings are the gloriously enlightening culmination of years of work[2], first heralded by Ada Yonath's report of crystals in 1980[3]. Others made significant contributions to the detailed structure of this machine, as poignantly summarized by Jeremy Berg, current Director of National Institute of General Medical Sciences, in his announcement

The Nobel committee has the daunting challenge of limiting itself to up to three laureates for each prize. Several other long-time NIGMS grantees who also contributed greatly to our understanding of the structure and function of the ribosome include Peter Moore, Harry Noller and Joachim Frank.

The American Society for Biochemistry and Molecular Biology posted an announcement of the prize echoing this sentiment as well.

Impact of Ribosome StructureImpact of Ribosome Structure

The ribosome ranks among the known structures with highest impact. Imagine the wonder and thrill at suddenly knowing how tens of proteins and large and small RNAs fit together into the elegant machines that serve as the protein factories in every cell and organelle of every organism on the planet. The immense size of the ribosome and each of the two individual ribosomal subunits that come together to form the complete ribosome that is active in translation made for a daunting task in structure determination. These structures were at the time they were first determined, and remain (in 2009), the largest asymmetric molecules solved crystallographically. In addition to providing us immense insight into the general molecular and atomic details of protein synthesis in every organism on earth, the development of new antibiotics are likely to rely on this ground-breaking work.

Ribosome ComponentsRibosome Components

The small subunit of the prokaryotic ribosome sediments at 30S[4]. It is composed of a 16S chain of RNA about 1,500 bases long (~500 kDa), plus about 20 protein chains. The proteins in the first small subunit determined range from about 3 kDa to 29 kDa.

The large subunit of the prokaryotic ribosome sediments at 50S. It is composed of two chains of RNA, a 23S chain (~3000 bases long, 946 kDa) and a 5S chain (~120 bases long, 39 kDa). Assembled with the RNA are about 30 protein chains. The proteins in the first large subunit determined range from 6 kDa to 37 kDa. See also Large Ribosomal Subunit of Haloarcula.

Other macromolecules in a functioning ribosome include three transfer RNA molecules, messenger RNA, and the nascent protein chain.

Thus, a complete functioning prokaryotic ribosome contains 7 RNA chains (including three tRNA's and one mRNA), 47 ribosomal protein chains, and one nascent protein chain. The total molecular mass is several million daltons.

The cytoplasmic ribosomes of eukaryotes are larger with more RNA and proteins. Eukaryotic cytoplasmic ribosomes also have an additional RNA in the large subunit, the 5.8S rRNA, that is about 150 nts and related to the 5' end of prokaryotic rRNA. In regards to the size, the ribosomal subunits of budding yeast and humans sediment at 40S and 60S; the complete ribosome sediments at 80S and it is generally about another million daltons larger than the prokaryotic one.

The Peptidyl Transferase Is A RibozymeThe Peptidyl Transferase Is A Ribozyme

The small subunit of the ribosome is the main site of decoding, directing the interaction of the messenger RNA codon with the anticodon stem-loops of the proper transfer RNA. The formation of peptide bonds occurs in the large subunit where the acceptor-stems of the tRNAs are docked. However, it is important to keep in mind that in the active ribosome the two subunits are in contact via bridges, and the actions in one subunit affect the other as the process of translation advances through the stages of initiation, elongation, and termination.

The initial determination of the atomic resolution structures of the subunits surprisingly revealed that RNA, but not protein, contributes directly to forming the site of both decoding and catalysis of peptide bond synthesis, with the ribosomal proteins only acting in an ancillary role, see ribozyme. (Examine the structural data concerning peptide bond synthesis here.) During the elongation stage of translation, new peptides are added to the carboxy-terminus of the growing nascent chain that is linked to the acceptor-end of the tRNA in the peptidyl or P site. As the nascent chain grows, it advances into a tunnel that passes through the large subunit, called the polypeptide exit tunnel. Several factors can interact at the site of extrusion of the nascent polypeptide chain to ensure proper folding or transport across a membrane. Additionally, during protein synthesis, many additional factors such as elongation factors (EF-Tu and EF-G) interact with the ribosome to elicit decoding and peptide bond synthesis accurately and efficiently. Structures of several of these factors in complex with the ribosome, as well as intermediate states in the process, are being observed now, building upon the first atomic structures.

First Atomic-Resolution Ribosome StructuresFirst Atomic-Resolution Ribosome Structures

The particular structures for which the Nobel prize was awarded were published in 2000 and were subsequently refined or improved upon. All these structures were determined using proteins from extremophiles. Here are the links to the Proteopedia entries:

  • Yonath lab original atomic-resolution structures[5][6]: Thermus thermophilus small ribosomal subunit - 1fka, improved in 1i94, 1i95, 1i96, and 1i97. Thermus thermophilus is a thermophilic eubacteria. Deinococcus radiodurans large ribosomal subunit - 1nkw, later refined to give 2zjr. Deinococcus radiodurans is a mesophilic eubacteria.
  • Ramakrishnan lab original atomic-resolution structures[7][8]: Thermus thermophilus small ribosomal subunit -1fjf which was later refined to 1j5e. Related: in complex with the antibiotics streptomycin, spectinomycin, and paromomycin in 1fjg; in complex with tetracycline in 1hnw, pactamycin in 1hnx, hygromycin B in 1hnz.

The Thermus thermophilus small ribosomal subunit is composed of a 16S chain of RNA about 1,522 bases long (494 kDa), plus 20 protein chains (S2-S20, THX). The protein chains range from 26 (THX, 3 kDa) to 256 amino acids (S2, 29 kDa).

  • Steitz and Moore labs original atomic-resolution structures[9][10]: Haloarcula marismortui large ribosomal subunit - 1ffk and later refined to give 1jj2, and then refined to give 1s72, and later 3cc2[11]. Related: 1ffz, 1fg0. Haloracula is a halophilic archaea. Assembled with the ribosomal RNAs (2,922 and 122 nucleotides long) in the structure are 27 protein chains (of a total of 31 known), varying in length from 49 (L39E, 6 kDa) to 337 amino acids (L3, 37 kDa).[12]

Proteopedia Topic Pages Covering the Ribosome and SubunitsProteopedia Topic Pages Covering the Ribosome and Subunits

Additional Ribosome StructuresAdditional Ribosome Structures

Several other ribosome structures have now been published, and here are just a few of these entries in Proteopedia (with apologies to the authors of those not yet listed):

  • 2j00 and 2j01 are the subunits of the 70S ribosome structure from the Ramakrishnan lab; the aminoglycoside antibiotic paromomycin is present as well. 2j02 and 2j02 form another molecule described in the accompanying report.
  • 1gix and 1giy are the subunits of the 70S ribosome structure determined by the Noller lab, the first for the 70S at near-atomic resolution; more of the mRNA chain is seen in 1jgo.
  • 2i2u and 2i2v are the subunits of the E. coli ribosome at 3.2 Å as solved by the Cate lab. 2i2t and 2i2p are related structures.
  • 2gya and 2gy9 are the subunits of a complete E. coli ribosome as determined by cryo-EM by Joachim Frank's lab.
  • 3u5b, 3u5c, 3u5d, 3u5e, 3u5f, 3u5g, 3u5h, and 3u5i are the subunits of the eukaryotic 80S ribosome of the baker's yeast Saccharomyces cerevisiae at a glorious 3.0 Å — including nearly all ribosomal RNA bases and protein side chains.
  • 1ibk is paromomycin bound to the small subunit.
  • 1ibm is the small subunit with an mRNA analog bound and an anticodon stem loop bound to the A site.
  • Small subunit bound to near-cognate tRNA anticodon stem-loop: 1n32, 1n33, 1n34, 1n36
  • 2ow8 and 1vsa are the subunits of a 70S-tRNA-mRNA complex from the Noller lab.
  • Macrolide, lincosamide, streptogramin B, and ketolide antibiotics bound to the large subunit, which impacts mechanisms of drug resistance:1yi2, 1yj2, 1yit, 1yhq, 1yjn, 1yij, and 1yj9
  • Refined H. marismortui 50S ribosomal subunit and its interaction with anisomycin and mutations outside the binding site that make it drug-resistant: 3cc2, 3cc4, 3cc7, 3cce, 3ccj, 3ccl, 3ccm, 3ccq, 3ccr 3ccs, 3ccu, 3ccv and 3cd6
  • Chloramphenicol bound to the H. marismortui 50S ribosomal subunit: 1nji
  • Chloramphenicol bound to the D. radiodurans 50S ribosomal subunit: 1k01
  • The antibiotic linezolid (example of the first new class of antibiotics to enter into clinical usage within the past 30 years) bound to the large ribosomal subunit of D. radiodurans: 3dll
  • Thiopeptide antibiotics bound to the large ribosomal subunit of D. radiodurans: 2zjp, 2zjq,and 3cf5
  • Macrolide antibiotics bound to the large ribosomal subunit of D. radiodurans: 2o43, 2o44, and 2o45
  • Ribosome Binding Domain of the Trigger Factor in complex with the large ribosomal subunit of D. radiodurans: 2d3o and 2aar
  • Initiation factor 1 bound to the small subunit: 1hr0
  • 4abr and 4abs show the Thermus thermophilus 50S ribosomal subunit bound by a tmRNA fragment, SmpB and elongation factor Tu at 3.2 Å as solved by the lab of V. Ramakrishnan.
  • 70S interaction with the Shine-Dalgarno sequence: 2qnh and 1vsp.
  • Ribosome Recycling Factor bound to the 70S Ribosome: 2v46, 2v47, 2v48, and 2v49
  • 2e5l shows the small subunit with an mRNA mimic bound and the Shine-Dalgarno and anti-Shine-Dalgarno sequences interacting.
  • 70S ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon: 2b64 and 2b66
  • Structures of the 30S bound with anticodon stem-loops from tRNAs that facilitate frame-shifting: 2uxb, 2uxc, and 2uxd
  • 70S Ribosome in complex with mRNA, paromomycin, acylated A- And P-Site tRNAs, and E-Site tRNA: 2wdg, 2wdh, 2wdi, 2wdj, 2wdk, 2wdl, 2wdm, and 2wdn
  • E. coli 70S ribosome in complex with paramomycin and ribosome recycling factor: 2qal, 2qam, 2qan, 2qao, 2qb9, 2qba, 2qbb, 2qbc, 2qbd, 2qbe, 2qbf, 2qbg, 2qbh, 2qbi, 2qbj, 2qbk, 2z4k, 2z4l, 2z4m, and 2z4n.
  • E. coli 70S ribosome intermediates in a key conformational change: 3i1m, 3i1n, 3i1o, 3i1p, 3i1q, 3i1r,3i1s,3i1t,3i1z, 3i20, 3i21, and 3i22.
  • E. coli ribosome in complex with the atypical aminoglycoside antibiotic hygromycin B: 3df1, 3df2,3df3, and 3df4.
  • Structural basis of a mechanism of hydrolytic release of the newly formed polypeptide by the large subunit that may be analogous to that used by release factors:3cma and 3cme
  • Elongation factor P bound to the 70S ribosome: 3huw, 3hux, 3huy, and 3huz.
  • Thermus thermophilus 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase): [2xfz],[2xg0],[2xg1], and [2xg2]
  • 70S ribosome in complex with Ef-Tu and and aminoacyl-tRNA (P- and E- site tRNAs are also present): 2wrn, 2wro, 2wrq, and 2wrr
  • 70S ribosome in complex with EF-G (P- and E- site tRNAs are also present): 2wri , 2wrj, 2wrk, and 2wrl
  • Structure of stalled ribosome rescuing factor, Yaej, bound to the Thermus thermophilus 70S Ribosome: 4dh9, 4dha, 4dhb, and 4dhc
  • EF-G–Ribosome Complexes (Thermus thermophilus) Trapped in Intermediate States of Translocation with β,γ-imidoguanosine 5′-triphosphate (GDPNP) or fusidic acid: 4kcy with GDPNP-I, 4kcz with GDPNP-I, 4kd0 with GDPNP-I, 4kd2 with GDPNP-I, 4kbt with GDPNP-2, 4kbu with GDPNP-2, 4kbv with GDPNP-2, 4kbw with GDPNP-2, 4kd8 with Fus-3.6, 4kd9 with Fus-3.6, 4kda with Fus-3.6, 4kdb with Fus-3.6, 4kdg with Fus-4.2, 4kdh with Fus-4.2, 4kdj with Fus-4.2, 4kdk with Fus-4.2
  • Elongation Factor G Bound to the Thermus thermophilus Ribosome in an Intermediate State of Translocation :4juw and 4jux
  • Control of Ribosomal Subunit Rotation by Elongation Factor G (Escherichia coli): 4kix, 4kiy, 4kiz, 4kj0, 4kj1, 4kj2, 4kj3, 4kj4, 4kj5, 4kj6, 4kj7, 4kj8, 4kj9, 4kja, 4kjb, and 4kjc
  • 3o2z, 3o30, 3o58, and 3o5h are the subunits of the eukaryotic 80S ribosome of the baker's yeast Saccharomyces cerevisiae.
  • The eukaryotic (S. cerevisiae) ribosome at atomic resolution using cryo-EM reconstruction and protein homology modeling: 3jyx, 3jyw, and 3jyv
  • The bacterial B. subtilis 50S ribosome assembly intermediates at atomic resolution using cryo-EM reconstruction:3j3v and 3j3w
  • Drosophila melanogaster 80S ribosome in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps: 3j38, 3j39, 3j3c, 3j3e
  • Human 80S ribosome in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps: 3j3a, 3j3b, 3j3d, 3j3f
  • High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome: 3zeq, 3zex,3zey, 3zf7
  • High-resolution cryo-electron microscopy structure of the large subunit of the mammalian mitochondrial ribosome: 4ce4
  • High-resolution cryo-electron microscopy structure of the large subunit of the yeast mitochondrial ribosome: 3j6b

See AlsoSee Also

ReferencesReferences

  1. ↑ Nobel Prizes for 3D Molecular Structure.
  2. ↑ Service RF. Chemistry Nobel. Honors to researchers who probed atomic structure of ribosomes. Science. 2009 Oct 16;326(5951):346-7. PMID:19833925 doi:326/5951/346
  3. ↑ Yonath A, Mussig J, Tesche B, Lorenz S, Erdmann VA, Wittmann HG. Crystallization of the large ribosomal subunits from Bacillus stearothermophilus. Biochem. Internat. 1980 1:428-435.
  4. ↑ Svedberg unit in Wikipedia
  5. ↑ Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell. 2000 Sep 1;102(5):615-23. PMID:11007480
  6. ↑ Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001 Nov 30;107(5):679-88. PMID:11733066
  7. ↑ Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327-39. PMID:11014182 doi:http://dx.doi.org/10.1038/35030006
  8. ↑ Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000 Sep 21;407(6802):340-8. PMID:11014183 doi:10.1038/35030019
  9. ↑ Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905-20. PMID:10937989
  10. ↑ Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science. 2000 Aug 11;289(5481):920-30. PMID:10937990
  11. ↑ Blaha G, Gurel G, Schroeder SJ, Moore PB, Steitz TA. Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. J Mol Biol. 2008 Jun 6;379(3):505-19. Epub 2008 Apr 8. PMID:18455733 doi:http://dx.doi.org/10.1016/j.jmb.2008.03.075
  12. ↑ Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905-20. PMID:10937989

Additional Literature and ResourcesAdditional Literature and Resources

[xtra 1][xtra 2][xtra 3][xtra 4][xtra 5][xtra 6][xtra 7][xtra 8][xtra 9][xtra 10]

  1. ↑ Moore PB. The ribosome returned. J Biol. 2009;8(1):8. Epub 2009 Jan 26. PMID:19222865 doi:10.1186/jbiol103
  2. ↑ Schmeing TM, Ramakrishnan V. What recent ribosome structures have revealed about the mechanism of translation. Nature. 2009 Oct 29;461(7268):1234-42. Epub 2009 Oct 18. PMID:19838167 doi:10.1038/nature08403
  3. ↑ Ramakrishnan V, Moore PB. Atomic structures at last: the ribosome in 2000. Curr Opin Struct Biol. 2001 Apr;11(2):144-54. PMID:11297922
  4. ↑ Rodnina MV, Wintermeyer W. The ribosome goes Nobel. Trends Biochem Sci. 2010 Jan;35(1):1-5. Epub 2009 Dec 2. PMID:19962317 doi:10.1016/j.tibs.2009.11.003
  5. ↑ Sprinzl M, Erdmann VA. Protein biosynthesis on ribosomes in molecular resolution: Nobel Prize for chemistry 2009 goes to three chemical biologists. Chembiochem. 2009 Dec 14;10(18):2851-3. PMID:19938030 doi:10.1002/cbic.200900652
  6. ↑ Bashan A, Yonath A. Correlating ribosome function with high-resolution structures. Trends Microbiol. 2008 Jul;16(7):326-35. Epub 2008 Jun 9. PMID:18547810 doi:10.1016/j.tim.2008.05.001
  7. ↑ Korostelev A, Noller HF. The ribosome in focus: new structures bring new insights. Trends Biochem Sci. 2007 Sep;32(9):434-41. Epub 2007 Aug 30. PMID:17764954 doi:10.1016/j.tibs.2007.08.002
  8. ↑ Steitz TA. A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol. 2008 Mar;9(3):242-53. PMID:18292779 doi:10.1038/nrm2352
  9. ↑ Zimmerman E, Yonath A. Biological implications of the ribosome's stunning stereochemistry. Chembiochem. 2009 Jan 5;10(1):63-72. PMID:19089882 doi:10.1002/cbic.200800554
  10. ↑ Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD. Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res. 2013 Jun 14. PMID:23771137 doi:10.1093/nar/gkt513

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